Biomolecular application

Though LI failed for general biomolecular applications [50], it has been found to be a useful ingredient in two other contexts macroscopic separable models, and enhanced sampling. 

P. Derreumaux, G. Zhang, B. Brooks, and T. Schlick. A truncated-Newton method adapted for CHARMM and biomolecular applications. J. Comp. Chem., 15 532-552, 1994. 

Watanabe, M., Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 99 (1995) 8063-8074 Figueirido, F., Levy, R. M., Zhou, R., Berne, B. J. Large Scale Simulation of Macromolecules in Solution Combining the Periodic Fast Multiple Method with Multiple Time Step Integrators. J. Chem. Phys. 106 (1997) 9835-9849 Derreumaux, P., Zhang, G., Schlick, T, Brooks, B.R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comp. Chem. 15 (1994) 532-555... 

In general, methods that couple local to global moves, of the types presented in this section, are expected to depend critically on the ability to exhaustively map all thermodynamically significant basins, which is not always guaranteed. However, these methods are likely to be used profitably in particular applications where only a small, known set of conformations are relevant (e.g., in biomolecular applications where sets of structures are known from X-ray or NMR data). 

Nathan A. Baker, Biomolecular Applications of Poisson-Boltzmann Methods. 

Hybrid solvation Implicit solvation plus Explicit solvation microsolvation subjected to the continuum method. Here the solute molecule is associated with explicit solvent molecules, usually no more than a few and sometimes as few as one, and with its bound (usually hydrogen-bonded) solvent molecule(s) is subjected to a continuum calculation. Such hybrid calculations have been used in attempts to improve values of solvation free energies in connection with pKp. [42], and also [45] and references therein. Other examples of the use of hybrid solvation are the hydration of the environmentally important hydroxyl radical [52] and of the ubiquitous alkali metal and halide ions [53]. Hybrid solvation has been surveyed in a review oriented toward biomolecular applications [54]. 

Chromatography suppliers offer affinity gels for a wide range of biomolecular applications. Availability... 

Although commonly used in the past, presaturation is becoming much less popular for biomolecular applications mainly due to the advent of more efficient methods (as discussed below) and also due to a number of shortcomings such as those listed below ... 

Molecular dynamics simulations have been used in a variety of ways. They can be used to compute mechanical moduli by studying the response of a model of the bulk polymer to a constant stress or strain, and to study the diffusion of molecules in membranes and polymers.There are numerous biomolecular applications. Structural, dynamic, and thermodynamic data from molecular dynamics have provided insights into the structure-function relationships, binding affinities, mobility, and stability of proteins, nucleic acids, and other macromolecules that cannot be obtained from static models. 

MALDI is particularly suited for use with time-of-flight analysers because pulsed lasers match well the ion introduction requirements of these instruments. In addition, the high mass ranges and short analysis times of these analysers make MALDI-time-of-flight the method of choice for many large biomolecular applications. Figure 3.13 is an example of a MALDI spectrum of a monoclonal antibody with a molecular weight of 149,000 (Hillenkamp and Karas, 1990). This spectrum is instructive in that it contains... 

If one accepts the continuum, linear response dielectric approximation for the solvent, then the Poisson equation of classical electrostatics provides an exact formalism for computing the electrostatic potential (r) produced by a molecular charge distribution p(r). The screening effects of salt can be added at this level via an approximate mean-field treatment, resulting in the so-called Poisson-Boltzmann (PB) equation [13]. In general, this is a second order non-linear partial differential equation, but its simpler linearized form is often used in biomolecular applications ... 

Baker, N.A. (2005) Biomolecular applications of Poisson-Boltzmann methods, in Reviews in Computational Chemistry, vol. 21 (eds K.B. Lipkowitz, R. Larter, and T.R. Cundari), John Wiley Sons Inc., pp. 349-379. 

When the tip is functionalized with a chemical species, chemical discrimination can be achieved (chemical force microscopy, CFM) [236, 237]. Covalently functionalized nanotubes can be prepared, allowing chemical contrast between areas with different SAM layers [238]. For biomolecular applications tips can be chemically modified by a layer of molecules that bind especially strongly to complementary molecules. Insight into mechanical properties of biomolecules, such as binding/recognition interactions, unfolding, and elasticity of complex biomolecules has been gained on the basis of force-distance curves [239-243]. 

The discussion of continuum electrostatics in Section 11.2.1 was limited to solution of Poisson s equation, which can be achieved exactly (for classical solutes) or to a good approximation (for QM solutes) using PCMs. In biomolecular applications, however, the objective is usually solution of the Poisson-Boltzmann equation [4, 33]. For low concentrations of dissolved ions, the latter is often replaced by the linearized Poisson-Boltzmann equation (LPBE),... 

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